/** * Gets the GATK samples database * * @link GenomeAnalysisEngine.getSampleDB * @return the GATK samples database or null if no genome analysis toolkit. */ public SampleDB getSampleDB() { if (toolkit == null) return null; else return toolkit.getSampleDB(); }
/** * Gets the master sequence dictionary for this walker * * @link GenomeAnalysisEngine.getMasterSequenceDictionary * @return the master sequence dictionary or null if no genome analysis toolkit. */ protected SAMSequenceDictionary getMasterSequenceDictionary() { if (toolkit == null) return null; else return toolkit.getMasterSequenceDictionary(); }
/** * Gets the GATK argument collection * * @link GenomeAnalysisEngine.getArguments * @return the GATK argument collection or null if no genome analysis toolkit. */ public GATKArgumentCollection getArguments() { if (toolkit == null) return null; else return toolkit.getArguments(); }